Jorrit Martijn Enserink

• Hermansen, Johanne Uthus; Kong, Weikaixin; Brodersen, Andrea M; Yanping, Yin; Urban, Aleksandra & Rein, Idun Dale [Show all 25 contributors for this article] (2026). A functional prognostic model predicts progression‐free survival in patients with relapsed chronic lymphocytic leukemia treated with ibrutinib + venetoclax. HemaSphere. 10(9). doi: 10.1002/hem3.70467. Full text in Research Archive Show summary

  Targeted therapies have improved outcomes for patients with chronic lymphocytic leukemia (CLL); yet, not all achieve durable responses. Existing prognostic models, developed for chemoimmunotherapy, have limited predictive value for newer targeted combinations. Here, we used data from a randomized phase II clinical trial to identify predictors of progression‐free survival (PFS) in response to Bruton tyrosine kinase (BTK) + B‐cell lymphoma 2 (Bcl‐2) inhibitor combination therapy. We studied the functional, genetic, and clinical characteristics of patients with relapsed/refractory (R/R) CLL treated with ibrutinib + venetoclax in the VISION/HO141 clinical trial (NCT03226301). Ex vivo drug sensitivity testing, (phospho)protein profiling, and immunophenotyping were performed on baseline peripheral blood mononuclear cells from 177 patients. Ex vivo drug sensitivity correlated with clinical responses to single‐agent therapies. (Phospho)protein patterns reflected intracellular pathway activity and predicted ex vivo drug sensitivity. Using stringent feature selection and regularized ridge regression to prevent overfitting, we integrated functional, genetic, and clinical data sets and identified six features—sensitivity to VEGFR‐2‐, JAK1/2 + Bcl‐2‐, and BTK + PI3K‐inhibitors; phosphorylation ratios of Bcl‐2:BTK and p90RSK:PLCγ2; and frequency of CD8 + T cells—that together outperformed the International Prognostic Index for CLL (CLL‐IPI) and other clinical scores in predicting PFS. These findings demonstrate that a prognostic model based on the functional features of CLL cell signaling and interaction with the microenvironment has the potential to improve upon conventional prognostic scores, warranting further clinical validation also in the frontline setting.

• Nothnagel, Patrizia Maria Christiane; Meslin, Paul-Arthur Richard; Wik, Jonas Aakre; Dufour, Damien; Strøm, Yunna Erika & Bjørås, Magnar [Show all 11 contributors for this article] (2026). Transient SUMOylation inhibition in human pre-adipocytes stably imprints a transcriptional beiging fate. Nucleic Acids Research (NAR). ISSN 0305-1048. 54(6), p. 1–22. doi: 10.1093/nar/gkag232. Full text in Research Archive Show summary

  SUMOylation regulates chromatin states and transcriptional programs that preserve cellular identity, yet how perturbation of the SUMOylation pathway impacts adipocyte plasticity remains unclear. Here, we show that brief pharmacologic inhibition of SUMOylation in human pre-adipocytes using TAK-981 primes stable de novo beige differentiation in the presence of the PPARG agonist rosiglitazone. Transient TAK-981 exposure produces changes in the transcriptome and metabolism of mature adipocytes, including robust induction of canonical beiging markers like UCP1 and increased mitochondrial respiration. Mechanistically, ATAC-seq and RNA-sequencing revealed immediate chromatin remodeling and early mobilization of CEBP family members, followed by stable activation of CEBPA and PPARG regulatory networks. ChIP experiments demonstrated loss of H3K27me3 and gain of H3K27ac at PPAR response elements at thermogenic enhancers, and increased PPARG occupancy across the UCP1 regulatory unit. This mechanism is enforced by enhanced cAMP-PKA-p38 signaling and stabilization of beiging transcription activators. We propose that transient relief of SUMO-mediated repression unlocks dominant regulatory units, notably the UCP1 enhancer cluster, producing a monomorphic reprogramming toward adaptive thermogenesis. These findings identify SUMOylation as a reversible epigenetic barrier to adipocyte beiging and suggest that temporally controlled SUMO pathway inhibition combined with PPARG activation could be exploited to modulate adipose tissue thermogenic capacity.

• Willoch-Allen, Katarina; Zhao, Zhi; Duran, Pilar Ayuda; Mikaeloff, Flora; Struyf, Nona & Österroos, Albin [Show all 13 contributors for this article] (2026). A multi-center study on the consistency of drug sensitivity testing in patients with acute myeloid leukemia. NPJ precision oncology. 10(1). doi: 10.1038/s41698-026-01480-4. Full text in Research Archive Show summary

  Clinical implementation of patient cell-based drug testing is hampered by inconsistencies and irreproducible results. Using linear mixed models and drug response data from four cohorts of patients with acute myeloid leukemia (n = 993 samples), we identified sources of variability in ex vivo drug sensitivity testing across the studies. We identified several experimental factors, including the time until sample was tested, the type of culture media and viability assay, which led to systematic differences in drug sensitivity profiles. We further investigated the effects of sample types (fresh or frozen) and disease status (diagnosis, relapse, or refractory), and observed that peripheral blood samples resulted in higher drug sensitivity levels, compared to those derived from bone marrow. Technical factors, such as the type of plate reader and centrifugation procedure, further contributed to the response variability depending on the chosen drug response metric. These factors need to be standardized for improved consistency in functional precision medicine studies.

• Balaguera, Nathalia Chica; Andersen, Aram Nikolai; Munoz, Sara Orellana; Llorente, Ignacio Garcia; P, Aurélie Nguéa & Nakken, Sigve [Show all 14 contributors for this article] (2026). Time-resolved functional genomics using deep learning reveals global hierarchical control of autophagy. Nature Cell Biology. ISSN 1465-7392. 28(3), p. 465–479. doi: 10.1038/s41556-025-01837-0. Full text in Research Archive Show summary

  Recycling of cellular components through autophagy maintains homeostasis in changing nutrient environments. Although its core mechanisms are extensively studied, understanding of its systems-wide dynamic regulation remains limited, particularly regarding how autophagy is inactivated once nutrients are restored. Here we mapped the genetic network that controls activation and inactivation of autophagy during nitrogen changes by combining time-resolved high-content imaging, deep learning and latent feature analysis. This dataset, termed AutoDRY, categorizes 5,919 mutants based on nutrient response kinetics and their contributions to autophagosome formation and clearance. Integrating these profiles with functional and genetic network data uncovered hierarchical and multilayered control of autophagy and revealed multiple new regulatory pathways. Notably, we identified the retrograde pathway as a pivotal time-varying modulator that tunes the expression of core autophagy genes and plays a central role in autophagy inactivation. Together, this study establishes a systems-level resource to guide future investigations of autophagy.

• Enserink, Jorrit Martijn & Balaguera, Nathalia Chica (2026). AutoDRY: a genome-wide resource revealing phase-specific control of autophagy activation, amplitude, and termination. Autophagy. ISSN 1554-8627. doi: 10.1080/15548627.2026.2660121. Full text in Research Archive
• Nothnagel, Patrizia Maria Christiane; Meslin, Paul-Arthur Richard; Wik, Jonas Aakre; Strøm, Yunna Erika; Bjørås, Magnar & Enserink, Jorrit [Show all 10 contributors for this article] (2025). Transient SUMOylation Inhibition In Human Pre-adipocytes Stably Imprints a Transcriptional Beiging Fate. bioRxiv (preprint article). 54(6). doi: 10.1101/2025.03.07.642034. Full text in Research Archive Show summary

  Abstract SUMOylation regulates chromatin states and transcriptional programs that preserve cellular identity, yet how transient perturbation of the SUMO pathway impacts adipocyte plasticity remains unclear. Here we show that brief pharmacologic inhibition of SUMO conjugation in human pre-adipocytes using TAK-981 primes stable de novo beige differentiation in the presence of the PPARG agonist rosiglitazone. Transient TAK-981 exposure before adipogenic induction produces long-lasting changes in the transcriptome and metabolism of mature adipocytes, including robust induction of canonical beiging markers like UCP1 and increased mitochondrial respiration. Mechanistically, ATAC-seq and transcription factor footprinting revealed immediate and durable chromatin remodeling and early mobilization of CEBP family members, followed by stable activation of CEBPA and PPARG regulatory networks. ChIP experiments demonstrated loss of H3K27me3 and gain of H3K27ac at PPAR response elements within key thermogenic enhancers, with increased PPARG occupancy across the UCP1 regulatory unit. This mechanism is enforced by enhanced cAMP-PKA-p38 signaling, and stabilization of beiging transcriptional activators. Our data support a model in which transient relief of SUMO-mediated repression unlocks dominant regulatory units, notably the UCP1 enhancer cluster, producing a monomorphic, cell type specific reprogramming toward adaptive thermogenesis. These findings identify SUMOylation as a reversible epigenetic barrier to adipocyte beiging and suggest that temporally controlled SUMO pathway inhibition combined with PPARG activation could be exploited to modulate adipose tissue thermogenic capacity. Graphical abstract SUMOylation restricts de novo differentiation of pre-adipocytes into beige adipocytes by repressing cAMP signaling and preventing epigenetic and transcriptional reprogramming of white adipocytes.

• Andresen, Siri; Outa, Amani al; Formica, Miriam; Enserink, Jorrit & Knævelsrud, Helene (2025). Improved detection of lipidated Atg8a by immunoblotting in Drosophila melanogaster cells and tissues enables precise investigation of Atg8a flux and its termination. Autophagy. ISSN 1554-8627. 21(11), p. 2497–2517. doi: 10.1080/15548627.2025.2508551. Full text in Research Archive Show summary

  Macroautophagy/autophagy is an essential intracellular catabolic process for maintaining cellularhomeostasis. In Drosophila melanogaster, Atg8a lipidation serves as a key marker for autophagy, yettraditional methods often fail to effectively detect its lipidated state. To overcome this limitation, wedeveloped a refined approach that employs N-ethylmaleimide (NEM) to inhibit Atg4, thereby pre-serving Atg8a lipidation during sample preparation both in vitro and in vivo. We determined theoptimal concentration of the autophagic inhibitors bafilomycin A1 (BafA1) and chloroquine (CQ)required for inhibition of autolysosomal degradation. Furthermore, we investigated the effects ofprolonged nutrient deprivation on autophagic flux and TORC1 signaling. Our findings not onlyvalidate the effectiveness of this new approach to monitor lipidation of Atg8a but also provideinsights into selection of autolysosomal inhibitors and nutrient-dependent regulatory roles of TORC1in Drosophila.

• Caulier, Benjamin William; Joaquina, Sandy; Gelebart, Pascal Francois; Dowling, Tara Helen Steinsland; Kaveh, Fatemeh & Thomas, Moritz [Show all 20 contributors for this article] (2024). CD37 is a safe chimeric antigen receptor target to treat acute myeloid leukemia. Cell Reports Medicine. 5(6). doi: 10.1016/j.xcrm.2024.101572. Full text in Research Archive Show summary

  Acute myeloid leukemia (AML) is characterized by the accumulation of immature myeloid cells in the bone marrow and the peripheral blood. Nearly half of the AML patients relapse after standard induction therapy, and new forms of therapy are urgently needed. Chimeric antigen receptor (CAR) T therapy has so far not been successful in AML due to lack of efficacy and safety. Indeed, the most attractive antigen targets are stem cell markers such as CD33 or CD123. We demonstrate that CD37, a mature B cell marker, is expressed in AML samples, and its presence correlates with the European LeukemiaNet (ELN) 2017 risk stratification. We repurpose the anti-lymphoma CD37CAR for the treatment of AML and show that CD37CAR T cells specifically kill AML cells, secrete proinflammatory cytokines, and control cancer progression in vivo. Importantly, CD37CAR T cells display no toxicity toward hematopoietic stem cells. Thus, CD37 is a promising and safe CAR T cell AML target.

• Wu, Chenyu; Gunnarsson, Einar Bjarki; Myklebust, Even Moa; Luque, Alvaro Kohn; Tadele, Dagim Shiferaw & Enserink, Jorrit [Show all 9 contributors for this article] (2024). Using birth-death processes to infer tumor subpopulation structure from live-cell imaging drug screening data. PLoS Computational Biology. ISSN 1553-734X. 20(3). doi: 10.1371/journal.pcbi.1011888. Full text in Research Archive Show summary

  Tumor heterogeneity is a complex and widely recognized trait that poses significant challenges in developing effective cancer therapies. In particular, many tumors harbor a variety of subpopulations with distinct therapeutic response characteristics. Characterizing this heterogeneity by determining the subpopulation structure within a tumor enables more precise and successful treatment strategies. In our prior work, we developed PhenoPop, a computational framework for unravelling the drug-response subpopulation structure within a tumor from bulk high-throughput drug screening data. However, the deterministic nature of the underlying models driving PhenoPop restricts the model fit and the information it can extract from the data. As an advancement, we propose a stochastic model based on the linear birth-death process to address this limitation. Our model can formulate a dynamic variance along the horizon of the experiment so that the model uses more information from the data to provide a more robust estimation. In addition, the newly proposed model can be readily adapted to situations where the experimental data exhibits a positive time correlation. We test our model on simulated data (in silico) and experimental data (in vitro), which supports our argument about its advantages.

• Corrales, Jeanne Gaspar; Alonso, Lucia Ramos; González-Sabín, Javier; Ríos-Lombardía, Nicolás; Trevijano-Contador, Nuria & Berg, Henriette Engen [Show all 12 contributors for this article] (2024). Characterization of a selective, iron-chelating antifungal compound that disrupts fungal metabolism and synergizes with fluconazole. Microbiology spectrum. 12(2). doi: 10.1128/spectrum.02594-23. Full text in Research Archive Show summary

  Fungal infections are a growing global health concern due to the limited number of available antifungal therapies as well as the emergence of fungi that are resistant to first-line antimicrobials, particularly azoles and echinocandins. Development of novel, selective antifungal therapies is challenging due to similarities between fungal and mammalian cells. An attractive source of potential antifungal treatments is provided by ecological niches co-inhabited by bacteria, fungi, and multicellular organisms, where complex relationships between multiple organisms have resulted in evolution of a wide variety of selective antimicrobials. Here, we characterized several analogs of one such natural compound, collismycin A. We show that NR-6226C has antifungal activity against several pathogenic Candida species, including C. albicans and C. glabrata, whereas it only has little toxicity against mammalian cells. Mechanistically, NR-6226C selectively chelates iron, which is a limiting factor for pathogenic fungi during infection. As a result, NR-6226C treatment causes severe mitochondrial dysfunction, leading to formation of reactive oxygen species, metabolic reprogramming, and a severe reduction in ATP levels. Using an in vivo model for fungal infections, we show that NR-6226C significantly increases survival of Candida-infected Galleria mellonella larvae. Finally, our data indicate that NR-6226C synergizes strongly with fluconazole in inhibition of C. albicans. Taken together, NR-6226C is a promising antifungal compound that acts by chelating iron and disrupting mitochondrial functions.

• Fuentes-Martín, Raúl; Duran, Pilar Ayuda; Hanes, Robert; Gallego-Yerga, Laura; Wolterinck, Lisanne & Enserink, Jorrit [Show all 8 contributors for this article] (2024). Promising anti-proliferative indolic benzenesulfonamides alter mechanisms with sulfonamide nitrogen substituents. European Journal of Medicinal Chemistry. ISSN 0223-5234. 275, p. 1–20. doi: 10.1016/j.ejmech.2024.116617. Full text in Research Archive Show summary

  Agents that cause apoptotic cell death by interfering with tubulin dynamics, such as vinblastine and paclitaxel, are an important class of chemotherapeutics. Unfortunately, these compounds are substrates for multidrug resistance (MDR) pumps, allowing cancer cells to gain resistance to these chemotherapeutics. The indolesulfonamide family of tubulin inhibitors are not excluded by MDR pumps and have a promising activity profile, although their high lipophilicity is a pharmacokinetic limitation for their clinical use. Here we present a new family of N-indolyl-3,4,5-trimethoxybenzenesulfonamide derivatives with modifications on the indole system at positions 1 and 3 and on the sulfonamide nitrogen. We synthesized and screened against HeLa cells 34 novel indolic benzenesulfonamides. The most potent derivatives (1.7–109 nM) were tested against a broad panel of cancer cell lines, which revealed that substituted benzenesulfonamides analogs had highest potency. Importantly, these compounds were only moderately toxic to non-tumorigenic cells, suggesting the presence of a therapeutic index. Consistent with known clinical anti-tubulin agents, these compounds arrested the cell cycle at G2/M phase. Mechanistically, they induced apoptosis via caspase 3/7 activation, which occurred during M arrest. The substituents on the sulfonamide nitrogen appeared to determine different mechanistic results and cell fates. These results suggest that the compounds act differently depending on the bridge substituents, thus making them very interesting as mechanistic probes as well as potential drugs for further development.

• Johannessen, Julie Aarmo; Formica, Miriam; Haukeland, Aina Louise C.; Bråthen, Nora Rojahn; Outa, Amani al & Larsen, Miriam Aarsund [Show all 9 contributors for this article] (2023). The human leukemic oncogene MLL-AF4 promotes hyperplastic growth of hematopoietic tissues in Drosophila larvae. iScience. 26(10). doi: 10.1016/j.isci.2023.107726. Full text in Research Archive Show summary

  MLL-rearranged (MLL-r) leukemias are among the leukemic subtypes with poorest survival, and treatment options have barely improved over the last decades. Despite increasing molecular understanding of the mechanisms behind these hematopoietic malignancies, this knowledge has had poor translation into the clinic. Here, we report a Drosophila melanogaster model system to explore the pathways affected in MLL-r leukemia. We show that expression of the human leukemic oncogene MLL-AF4 in the Drosophila hematopoietic system resulted in increased levels of circulating hemocytes and an enlargement of the larval hematopoietic organ, the lymph gland. Strikingly, depletion of Drosophila orthologs of known interactors of MLL-AF4, such as DOT1L, rescued the leukemic phenotype. In agreement, treatment with small-molecule inhibitors of DOT1L also prevented the MLL-AF4-induced leukemia-like phenotype. Taken together, this model provides an in vivo system to unravel the genetic interactors involved in leukemogenesis and offers a system for improved biological understanding of MLL-r leukemia.

• Alonso, Lucia Ramos; Holland, Petter; Gras, Stéphanie Le; Zhao, Xu; Jost, Bernard & Bjørås, Magnar [Show all 9 contributors for this article] (2023). Mitotic chromosome condensation resets chromatin to safeguard transcriptional homeostasis during interphase. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 120(4). doi: 10.1073/pnas.2210593120. Full text in Research Archive Show summary

  Mitotic entry correlates with the condensation of the chromosomes, changes in histone modifications, exclusion of transcription factors from DNA, and the broad downregulation of transcription. However, whether mitotic condensation influences transcription in the subsequent interphase is unknown. Here, we show that preventing one chromosome to condense during mitosis causes it to fail resetting of transcription. Rather, in the following interphase, the affected chromosome contains unusually high levels of the transcription machinery, resulting in abnormally high expression levels of genes in cis, including various transcription factors. This subsequently causes the activation of inducible transcriptional programs in trans, such as the GAL genes, even in the absence of the relevant stimuli. Thus, mitotic chromosome condensation exerts stringent control on interphase gene expression to ensure the maintenance of basic cellular functions and cell identity across cell divisions. Together, our study identifies the maintenance of transcriptional homeostasis during interphase as an unexpected function of mitosis and mitotic chromosome condensation.

• Outa, Amani al; Hicks, Steven; Thambawita, Vajira L B; Andresen, Siri; Enserink, Jorrit Martijn & Halvorsen, Pål [Show all 8 contributors for this article] (2023). CELLULAR, A Cell Autophagy Imaging Dataset. Scientific Data. doi: 10.1038/s41597-023-02687-x. Full text in Research Archive Show summary

  Cells in living organisms are dynamic compartments that continuously respond to changes in their environment to maintain physiological homeostasis. While basal autophagy exists in cells to aid in the regular turnover of intracellular material, autophagy is also a critical cellular response to stress, such as nutritional depletion. Conversely, the deregulation of autophagy is linked to several diseases, such as cancer, and hence, autophagy constitutes a potential therapeutic target. Image analysis to follow autophagy in cells, especially on high-content screens, has proven to be a bottleneck. Machine learning (ML) algorithms have recently emerged as crucial in analyzing images to efficiently extract information, thus contributing to a better understanding of the questions at hand. This paper presents CELLULAR, an open dataset consisting of images of cells expressing the autophagy reporter mRFP-EGFP-Atg8a with cell-specific segmentation masks. Each cell is annotated into either basal autophagy, activated autophagy, or unknown. Furthermore, we introduce some preliminary experiments using the dataset that can be used as a baseline for future research.

• Chen, Yingjia; He, Liye; Ianevski, Aleksandr; Duran, Pilar Ayuda; Potdar, Swapnil & Saarela, Jani [Show all 14 contributors for this article] (2023). Robust scoring of selective drug responses for patient-tailored therapy selection. Nature Protocols. ISSN 1754-2189. p. 1–30. doi: 10.1038/s41596-023-00903-x. Full text in Research Archive Show summary

  Most patients with advanced malignancies are treated with severely toxic, first-line chemotherapies. Personalized treatment strategies have led to improved patient outcomes and could replace one-size-fits-all therapies, yet they need to be tailored by testing of a range of targeted drugs in primary patient cells. Most functional precision medicine studies use simple drug-response metrics, which cannot quantify the selective effects of drugs (i.e., the differential responses of cancer cells and normal cells). We developed a computational method for selective drug-sensitivity scoring (DSS), which enables normalization of the individual patient’s responses against normal cell responses. The selective response scoring uses the inhibition of noncancerous cells as a proxy for potential drug toxicity, which can in turn be used to identify effective and safer treatment options. Here, we explain how to apply the selective DSS calculation for guiding precision medicine in patients with leukemia treated across three cancer centers in Europe and the USA; the generic methods are also widely applicable to other malignancies that are amenable to drug testing. The open-source and extendable R-codes provide a robust means to tailor personalized treatment strategies on the basis of increasingly available ex vivo drug-testing data from patients in real-world and clinical trial settings. We also make available drug-response profiles to 527 anticancer compounds tested in 10 healthy bone marrow samples as reference data for selective scoring and de-prioritization of drugs that show broadly toxic effects. The procedure takes <60 min and requires basic skills in R.

• Andersen, Aram Nikolai; Brodersen, Andrea M; Duran, Pilar Ayuda; Piechaczyk, Laure Isabelle; Tadele, Dagim Shiferaw & Baken, Lizet [Show all 12 contributors for this article] (2023). Clinical forecasting of acute myeloid leukemia using ex vivo drug-sensitivity profiling. Cell Reports Methods. 3(12), p. 1–16. doi: 10.1016/j.crmeth.2023.100654. Full text in Research Archive Show summary

  Current treatment selection for acute myeloid leukemia (AML) patients depends on risk stratification based on cytogenetic and genomic markers. However, the forecasting accuracy of treatment response remains modest, with most patients receiving intensive chemotherapy. Recently, ex vivo drug screening has gained traction in personalized treatment selection and as a tool for mapping patient groups based on relevant cancer dependencies. Here, we systematically evaluated the use of drug sensitivity profiling for predicting patient survival and clinical response to chemotherapy in a cohort of AML patients. We compared computational methodologies for scoring drug efficacy and characterized tools to counter noise and batch-related confounders pervasive in high-throughput drug testing. We show that ex vivo drug sensitivity profiling is a robust and versatile approach to patient prognostics that comprehensively maps functional signatures of treatment response and disease progression. In conclusion, ex vivo drug profiling can assess risk for individual AML patients and may guide clinical decision-making.

• Duran, Pilar Ayuda; Hermansen, Johanne Uthus; Giliberto, Mariaserena; Yin, Yanping; Hanes, Robert & Gordon, Sandra [Show all 13 contributors for this article] (2023). Standardized assays to monitor drug sensitivity in hematologic cancers. Cell death discovery. 9(1), p. 1–13. doi: 10.1038/s41420-023-01722-5. Full text in Research Archive Show summary

  Abstract The principle of drug sensitivity testing is to expose cancer cells to a library of different drugs and measure its effects on cell viability. Recent technological advances, continuous approval of targeted therapies, and improved cell culture protocols have enhanced the precision and clinical relevance of such screens. Indeed, drug sensitivity testing has proven diagnostically valuable for patients with advanced hematologic cancers. However, different cell types behave differently in culture and therefore require optimized drug screening protocols to ensure that their ex vivo drug sensitivity accurately reflects in vivo drug responses. For example, primary chronic lymphocytic leukemia (CLL) and multiple myeloma (MM) cells require unique microenvironmental stimuli to survive in culture, while this is less the case for acute myeloid leukemia (AML) cells. Here, we present our optimized and validated protocols for culturing and drug screening of primary cells from AML, CLL, and MM patients, and a generic protocol for cell line models. We also discuss drug library designs, reproducibility, and quality controls. We envision that these protocols may serve as community guidelines for the use and interpretation of assays to monitor drug sensitivity in hematologic cancers and thus contribute to standardization. The read-outs may provide insight into tumor biology, identify or confirm treatment resistance and sensitivity in real time, and ultimately guide clinical decision-making.

• Tislevoll, Benedicte Sjo; Hellesøy, Monica; Fagerholt, Oda Helen Eck; Gullaksen, Stein-Erik; Srivastava, Aashish & Birkeland, Even [Show all 24 contributors for this article] (2023). Early response evaluation by single cell signaling profiling in acute myeloid leukemia. Nature Communications. 14(1). doi: 10.1038/s41467-022-35624-4. Full text in Research Archive Show summary

  Aberrant pro-survival signaling is a hallmark of cancer cells, but the response to chemotherapy is poorly understood. In this study, we investigate the initial signaling response to standard induction chemotherapy in a cohort of 32 acute myeloid leukemia (AML) patients, using 36-dimensional mass cytometry. Through supervised and unsupervised machine learning approaches, we find that reduction of extracellular-signal-regulated kinase (ERK) 1/2 and p38 mitogen-activated protein kinase (MAPK) phosphorylation in the myeloid cell compartment 24 h post-chemotherapy is a significant predictor of patient 5-year overall survival in this cohort. Validation by RNA sequencing shows induction of MAPK target gene expression in patients with high phospho-ERK1/2 24 h post-chemotherapy, while proteomics confirm an increase of the p38 prime target MAPK activated protein kinase 2 (MAPKAPK2). In this study, we demonstrate that mass cytometry can be a valuable tool for early response evaluation in AML and elucidate the potential of functional signaling analyses in precision oncology diagnostics.

• Luque, Alvaro Kohn; Myklebust, Even Moa; Tadele, Dagim Shiferaw; Giliberto, Mariaserena; Schmiester, Leonard & Noory, Jasmine [Show all 15 contributors for this article] (2023). Phenotypic deconvolution in heterogeneous cancer cell populations using drug-screening data. Cell Reports Methods. 3(3). doi: 10.1016/j.crmeth.2023.100417. Full text in Research Archive Show summary

  Tumor heterogeneity is an important driver of treatment failure in cancer since therapies often select for drug-tolerant or drug-resistant cellular subpopulations that drive tumor growth and recurrence. Profiling the drug-response heterogeneity of tumor samples using traditional genomic deconvolution methods has yielded limited results, due in part to the imperfect mapping between genomic variation and functional characteristics. Here, we leverage mechanistic population modeling to develop a statistical framework for profiling phenotypic heterogeneity from standard drug-screen data on bulk tumor samples. This method, called PhenoPop, reliably identifies tumor subpopulations exhibiting differential drug responses and estimates their drug sensitivities and frequencies within the bulk population. We apply PhenoPop to synthetically generated cell populations, mixed cell-line experiments, and multiple myeloma patient samples and demonstrate how it can provide individualized predictions of tumor growth under candidate therapies. This methodology can also be applied to deconvolution problems in a variety of biological settings beyond cancer drug response.

• Hanes, Robert; Ayuda-Duran, Maria del Pilar; Rønneberg, Leiv; Nakken, Sigve; Hovig, Eivind & Zucknick, Manuela [Show all 7 contributors for this article] (2022). screenwerk: a modular tool for the design and analysis of drug combination screens. Bioinformatics. ISSN 1367-4803. 39(1). doi: 10.1093/bioinformatics/btac840. Full text in Research Archive Show summary

  Abstract Motivation There is a rapidly growing interest in high-throughput drug combination screening to identify synergizing drug interactions for treatment of various maladies, such as cancer and infectious disease. This creates the need for pipelines that can be used to design such screens, perform quality control on the data and generate data files that can be analyzed by synergy-finding bioinformatics applications. Results screenwerk is an open-source, end-to-end modular tool available as an R-package for the design and analysis of drug combination screens. The tool allows for a customized build of pipelines through its modularity and provides a flexible approach to quality control and data analysis. screenwerk is adaptable to various experimental requirements with an emphasis on precision medicine. It can be coupled to other R packages, such as bayesynergy, to identify synergistic and antagonistic drug interactions in cell lines or patient samples. screenwerk is scalable and provides a complete solution for setting up drug sensitivity screens, read raw measurements and consolidate different datasets, perform various types of quality control and analyze, report and visualize the results of drug sensitivity screens. Availability and implementation The R-package and technical documentation is available at https://github.com/Enserink-lab/screenwerk; the R source code is publicly available at https://github.com/Enserink-lab/screenwerk under GNU General Public License v3.0; bayesynergy is accessible at https://github.com/ocbe-uio/bayesynergy. Selected modules are available through Galaxy, an open-source platform for FAIR data analysis at https://oncotools.elixir.no Supplementary information Supplementary data are available at Bioinformatics online.

• Zhao, Xu; Hendriks, Ivo A; Gras, Stephanie Le; Ye, Tao; Alonso, Lucia Ramos & P, Aurélie Nguéa [Show all 13 contributors for this article] (2022). Waves of sumoylation support transcription dynamics during adipocyte differentiation. Nucleic Acids Research (NAR). ISSN 0305-1048. 50(3), p. 1351–1369. doi: 10.1093/nar/gkac027. Full text in Research Archive Show summary

  Abstract Tight control of gene expression networks required for adipose tissue formation and plasticity is essential for adaptation to energy needs and environmental cues. However, the mechanisms that orchestrate the global and dramatic transcriptional changes leading to adipocyte differentiation remain to be fully unraveled. We investigated the regulation of nascent transcription by the sumoylation pathway during adipocyte differentiation using SLAMseq and ChIPseq. We discovered that the sumoylation pathway has a dual function in differentiation; it supports the initial downregulation of pre-adipocyte-specific genes, while it promotes the establishment of the mature adipocyte transcriptional program. By characterizing endogenous sumoylome dynamics in differentiating adipocytes by mass spectrometry, we found that sumoylation of specific transcription factors like PPARγ/RXR and their co-factors are associated with the transcription of adipogenic genes. Finally, using RXR as a model, we found that sumoylation may regulate adipogenic transcription by supporting the chromatin occurrence of transcription factors. Our data demonstrate that the sumoylation pathway supports the rewiring of transcriptional networks required for formation of functional adipocytes. This study also provides the scientists in the field of cellular differentiation and development with an in-depth resource of the dynamics of the SUMO-chromatin landscape, SUMO-regulated transcription and endogenous sumoylation sites during adipocyte differentiation.

• Enserink, Jorrit & Chymkowitch, Pierre (2022). Cell Cycle-Dependent Transcription: The Cyclin Dependent Kinase Cdk1 Is a Direct Regulator of Basal Transcription Machineries. International Journal of Molecular Sciences. ISSN 1661-6596. 23(3), p. 1–23. doi: 10.3390/ijms23031293. Full text in Research Archive Show summary

  The cyclin-dependent kinase Cdk1 is best known for its function as master regulator of the cell cycle. It phosphorylates several key proteins to control progression through the different phases of the cell cycle. However, studies conducted several decades ago with mammalian cells revealed that Cdk1 also directly regulates the basal transcription machinery, most notably RNA polymerase II. More recent studies in the budding yeast Saccharomyces cerevisiae have revisited this function of Cdk1 and also revealed that Cdk1 directly controls RNA polymerase III activity. These studies have also provided novel insight into the physiological relevance of this process. For instance, cell cycle-stage-dependent activity of these complexes may be important for meeting the increased demand for various proteins involved in housekeeping, metabolism, and protein synthesis. Recent work also indicates that direct regulation of the RNA polymerase II machinery promotes cell cycle entry. Here, we provide an overview of the regulation of basal transcription by Cdk1, and we hypothesize that the original function of the primordial cell-cycle CDK was to regulate RNAPII and that it later evolved into specialized kinases that govern various aspects of the transcription machinery and the cell cycle.

• Alonso, Lucia Ramos; Llorente, Ignacio Garcia; Enserink, Jorrit & Chymkowitch, Pierre (2022). Analysis of the pheromone signaling pathway by RT-qPCR in the budding yeast Saccharomyces cerevisiae. STAR Protocols. 3(1). doi: 10.1016/j.xpro.2022.101210. Full text in Research Archive Show summary

  FUS3 and STE2 expression levels can be used as reporters for signaling through the pheromone pathway in the budding yeast Saccharomyces cerevisiae. Here, we describe an optimized protocol to measure the expression levels of FUS3 and STE2 using quantitative reverse transcription PCR (RT-qPCR). We describe the steps for comparing untreated and pheromone-treated yeast cells and how to quantify the changes in various deletion strains. The protocol can be applied to determine potential regulators of the pheromone pathway. For complete details on the use and execution of this protocol, please refer to Garcia et al. (2021).

• Caulier, Benjamin William; Enserink, Jorrit & Wälchli, Sébastien (2021). Pharmacologic control of CAR T cells. International Journal of Molecular Sciences. ISSN 1661-6596. 22(9), p. 1–23. doi: 10.3390/ijms22094320. Full text in Research Archive Show summary

  Chimeric antigen receptor (CAR) therapy is a promising modality for the treatment of advanced cancers that are otherwise incurable. During the last decade, different centers worldwide have tested the anti-CD19 CAR T cells and shown clinical benefits in the treatment of B cell tumors. However, despite these encouraging results, CAR treatment has also been found to lead to serious side effects and capricious response profiles in patients. In addition, the CD19 CAR success has been difficult to reproduce for other types of malignancy. The appearance of resistant tumor variants, the lack of antigen specificity, and the occurrence of severe adverse effects due to over-stimulation of the therapeutic cells have been identified as the major impediments. This has motivated a growing interest in developing strategies to overcome these hurdles through CAR control. Among them, the combination of small molecules and approved drugs with CAR T cells has been investigated. These have been exploited to induce a synergistic anti-cancer effect but also to control the presence of the CAR T cells or tune the therapeutic activity. In the present review, we discuss opportunistic and rational approaches involving drugs featuring anti-cancer efficacy and CAR-adjustable effect.

• Grad, Iwona; Hanes, Robert; Ayuda-Duran, Maria del Pilar; Kuijjer, Marieke Lydia; Enserink, Jorrit & Meza, Leonardo Zepeda [Show all 7 contributors for this article] (2021). Discovery of novel candidates for anti-liposarcoma therapies by medium-scale high-throughput drug screening. PLOS ONE. 16(3), p. 1–23. doi: 10.1371/journal.pone.0248140. Full text in Research Archive Show summary

  Sarcomas are a heterogeneous group of mesenchymal orphan cancers and new treatment alternatives beyond traditional chemotherapeutic regimes are much needed. So far, tumor mutation analysis has not led to significant treatment advances, and we have attempted to bypass this limitation by performing direct drug testing of a library of 353 anti-cancer compounds that are either FDA-approved, in clinical trial, or in advanced stages of preclinical development on a panel of 13 liposarcoma cell lines. We identified and validated six drugs, targeting different mechanisms and with good efficiency across the cell lines: MLN2238 –a proteasome inhibitor, GSK2126458 –a PI3K/mTOR inhibitor, JNJ-26481585 –a histone deacetylase inhibitor, triptolide–a multi-target drug, YM155 –a survivin inhibitor, and APO866 (FK866)–a nicotinamide phosphoribosyl transferase inhibitor. GR50s for those drugs were mostly in the nanomolar range, and in many cases below 10 nM. These drugs had long-lasting effect upon drug withdrawal, limited toxicity to normal cells and good efficacy also against tumor explants. Finally, we identified potential genomic biomarkers of their efficacy. Being approved or in clinical trials, these drugs are promising candidates for liposarcoma treatment.

• Klionsky, Daniel J.; Abdel-Aziz, Amal Kamal; Abdelfatah, Sara; Abdellatif, Mahmoud Khaled; Abdoli, Asghar & Abudu, Yakubu Princely [Show all 50 contributors for this article] (2021). Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy. ISSN 1554-8627. 17(1), p. 1–382. doi: https:/www.tandfonline.com/doi/full/10.1080/15548627.2020.1797280. Full text in Research Archive
• Rønneberg, Leiv; Cremaschi, Andrea; Hanes, Robert; Enserink, Jorrit & Zucknick, Manuela (2021). bayesynergy: flexible Bayesian modelling of synergistic interaction effects in in vitro drug combination experiments. Briefings in Bioinformatics. ISSN 1467-5463. 22(6), p. 1–12. doi: 10.1093/bib/bbab251. Full text in Research Archive Show summary

  Abstract The effect of cancer therapies is often tested pre-clinically via in vitro experiments, where the post-treatment viability of the cancer cell population is measured through assays estimating the number of viable cells. In this way, large libraries of compounds can be tested, comparing the efficacy of each treatment. Drug interaction studies focus on the quantification of the additional effect encountered when two drugs are combined, as opposed to using the treatments separately. In the bayesynergy R package, we implement a probabilistic approach for the description of the drug combination experiment, where the observed dose response curve is modelled as a sum of the expected response under a zero-interaction model and an additional interaction effect (synergistic or antagonistic). Although the model formulation makes use of the Bliss independence assumption, we note that the posterior estimates of the dose–response surface can also be used to extract synergy scores based on other reference models, which we illustrate for the Highest Single Agent model. The interaction is modelled in a flexible manner, using a Gaussian process formulation. Since the proposed approach is based on a statistical model, it allows the natural inclusion of replicates, handles missing data and uneven concentration grids, and provides uncertainty quantification around the results. The model is implemented in the open-source Stan programming language providing a computationally efficient sampler, a fast approximation of the posterior through variational inference, and features parallel processing for working with large drug combination screens.

• Llorente, Ignacio Garcia; Munoz, Sara Orellana; Alonso, Lucia Ramos; Andersen, Aram Nikolai; Zimmermann, Christine & Eriksson, Jens [Show all 11 contributors for this article] (2021). Kel1 is a phosphorylation-regulated noise suppressor of the pheromone signaling pathway. Cell reports. 37(13), p. 1–20. doi: 10.1016/j.celrep.2021.110186. Full text in Research Archive Show summary

  Mechanisms have evolved that allow cells to detect signals and generate an appropriate response. The accuracy of these responses relies on the ability of cells to discriminate between signal and noise. How cells filter noise in signaling pathways is not well understood. Here, we analyze noise suppression in the yeast pheromone signaling pathway and show that the poorly characterized protein Kel1 serves as a major noise suppressor and prevents cell death. At the molecular level, Kel1 prevents spontaneous activation of the pheromone response by inhibiting membrane recruitment of Ste5 and Far1. Only a hypophosphorylated form of Kel1 suppresses signaling, reduces noise, and prevents pheromone-associated cell death, and our data indicate that the MAPK Fus3 contributes to Kel1 phosphorylation. Taken together, Kel1 serves as a phospho-regulated suppressor of the pheromone pathway to reduce noise, inhibit spontaneous activation of the pathway, regulate mating efficiency, and prevent pheromone-associated cell death.

• Melvold, Katrine; Giliberto, Mariaserena; Karlsen, Linda; Ayuda-Duran, Maria del Pilar; Hanes, Robert & Holien, Toril [Show all 11 contributors for this article] (2021). Mcl-1 and Bcl-xL levels predict responsiveness to dual MEK/Bcl-2 inhibition in B-cell malignancies. Molecular Oncology. ISSN 1574-7891. p. 1–18. doi: 10.1002/1878-0261.13153. Full text in Research Archive Show summary

  Most patients with chronic lymphocytic leukemia (CLL) initially respond to targeted therapies, but eventually relapse and develop resistance. Novel treatment strategies are therefore needed to improve patient outcomes. Here, we performed direct drug testing on primary CLL cells and identified synergy between eight different mitogen-activated protein kinase kinase (MEK) inhibitors and the B-cell lymphoma 2 (Bcl-2) antagonist venetoclax. Drug sensitivity was independent of immunoglobulin heavy-chain gene variable region (IGVH) and tumor protein p53 (TP53) mutational status, and CLL cells from idelalisib-resistant patients remained sensitive to the treatment. This suggests that combined MEK/Bcl-2 inhibition may be an option for high-risk CLL. To test whether sensitivity could be detected in other B-cell malignancies, we performed drug testing on cell line models of CLL (n = 4), multiple myeloma (MM; n = 8), and mantle cell lymphoma (MCL; n = 7). Like CLL, MM cells were sensitive to the MEK inhibitor trametinib, and synergy was observed with venetoclax. In contrast, MCL cells were unresponsive to MEK inhibition. To investigate the underlying mechanisms of the disease-specific drug sensitivities, we performed flow cytometry-based high-throughput profiling of 31 signaling proteins and regulators of apoptosis in the 19 cell lines. We found that high expression of the antiapoptotic proteins myeloid cell leukemia-1 (Mcl-1) or B-cell lymphoma-extra large (Bcl-xL) predicted low sensitivity to trametinib + venetoclax. The low sensitivity could be overcome by combined treatment with an Mcl-1 or Bcl-xL inhibitor. Our findings suggest that MEK/Bcl-2 inhibition has therapeutic potential in leukemia and myeloma, and demonstrate that protein expression levels can serve as predictive biomarkers for treatment sensitivities.

• Tadele, Dagim Shiferaw; Robertson, Joseph; Crispin, Richard; Herrera, Carmen; Chlubnová, Markéta & Piechaczyk, Laure Isabelle [Show all 14 contributors for this article] (2020). A cell competition-based small molecule screen identifies a novel compound that induces dual c-Myc depletion and p53 activation. Journal of Biological Chemistry. ISSN 0021-9258. 296. doi: 10.1074/jbc.RA120.015285. Full text in Research Archive Show summary

  Breakpoint Cluster Region-Abelson kinase (BCR–Abl) is a driver oncogene that causes chronic myeloid leukemia and a subset of acute lymphoid leukemias. Although tyrosine kinase inhibitors provide an effective treatment for these diseases, they generally do not kill leukemic stem cells (LSCs), the cancer-initiating cells that compete with normal hematopoietic stem cells for the bone marrow niche. New strategies to target cancers driven by BCR–Abl are therefore urgently needed. We performed a small molecule screen based on competition between isogenic untransformed cells and BCR–Abl-transformed cells and identified several compounds that selectively impair the fitness of BCR–Abl-transformed cells. Interestingly, systems-level analysis of one of these novel compounds, DJ34, revealed that it induced depletion of c-Myc and activation of p53. DJ34-mediated c-Myc depletion occurred in a wide range of tumor cell types, including lymphoma, lung, glioblastoma, breast cancer, and several forms of leukemia, with primary LSCs being particularly sensitive to DJ34. Further analyses revealed that DJ34 interferes with c-Myc synthesis at the level of transcription, and we provide data showing that DJ34 is a DNA intercalator and topoisomerase II inhibitor. Physiologically, DJ34 induced apoptosis, cell cycle arrest, and cell differentiation. Taken together, we have identified a novel compound that dually targets c-Myc and p53 in a wide variety of cancers, and with particularly strong activity against LSCs.

• Omsland, Maria; Andresen, Vibeke; Gullaksen, Stein-Erik; Ayuda-Duran, Maria del Pilar; Popa, Mihaela Lucia & Hovland, Randi [Show all 10 contributors for this article] (2020). Tyrosine kinase inhibitors and interferon‐α increase tunneling nanotube (TNT) formation and cell adhesion in chronic myeloid leukemia (CML) cell lines (. The FASEB Journal. ISSN 0892-6638. 34(3), p. 3774–3791. doi: 10.1096/fj.201802061RR. Full text in Research Archive Show summary

  Chronic myeloid leukemia (CML) is a stem cell disease of the bone marrow where mechanisms of inter‐leukemic communication and cell‐to‐cell interactions are proposed to be important for optimal therapy response. Tunneling nanotubes (TNTs) are novel intercellular communication structures transporting different cargos with potential implications in therapy resistance. Here, we have investigated TNTs in CML cells and following treatment with the highly effective CML therapeutics tyrosine kinase inhibitors (TKIs) and interferon‐α (IFNα). CML cells from chronic phase CML patients as well as the blast crisis phase cell lines, Kcl‐22 and K562, formed few or no TNTs. Treatment with imatinib increased TNT formation in both Kcl‐22 and K562 cells, while nilotinib or IFNα increased TNTs in Kcl‐22 cells only where the TNT increase was associated with adherence to fibronectin‐coated surfaces, altered morphology, and reduced movement involving β1integrin. Ex vivo treated cells from chronic phase CML patients showed limited changes in TNT formation similarly to bone marrow cells from healthy individuals. Interestingly, in vivo nilotinib treatment in a Kcl‐22 subcutaneous mouse model resulted in morphological changes and TNT‐like structures in the tumor‐derived Kcl‐22 cells. Our results demonstrate that CML cells express low levels of TNTs, but CML therapeutics increase TNT formation in designated cell models indicating TNT functionality in bone marrow derived malignancies and their microenvironment.

• P, Aurélie Nguéa; Robertson, Joseph; Herrera, Maria Carmen; Chymkowitch, Pierre & Enserink, Jorrit (2019). Desumoylation of RNA polymerase III lies at the core of the Sumo stress response in yeast. Journal of Biological Chemistry. ISSN 0021-9258. 294(49), p. 18784–18795. doi: 10.1074/jbc.RA119.009721. Full text in Research Archive Show summary

  Post-translational modification by small ubiquitin-like modifier (Sumo) regulates many cellular processes, including the adaptive response to various types of stress, referred to as the Sumo stress response (SSR). However, it remains unclear whether the SSR involves a common set of core proteins regardless of the type of stress or whether each particular type of stress induces a stress-specific SSR that targets a unique, largely nonoverlapping set of Sumo substrates. In this study, we used MS and a Gene Ontology approach to identify differentially sumoylated proteins during heat stress, hyperosmotic stress, oxidative stress, nitrogen starvation, and DNA alkylation in Saccharomyces cerevisiae cells. Our results indicate that each stress triggers a specific SSR signature centered on proteins involved in transcription, translation, and chromatin regulation. Strikingly, whereas the various stress-specific SSRs were largely nonoverlapping, all types of stress tested here resulted in desumoylation of subunits of RNA polymerase III, which correlated with a decrease in tRNA synthesis. We conclude that desumoylation and subsequent inhibition of RNA polymerase III constitutes the core of all stress-specific SSRs in yeast.

• Prikrylova, Terezia; Robertson, Julia; Ferrucci, Francesca; Konorska, Dorota Joanna; Aanes, Håvard & Manaf, Adeel [Show all 16 contributors for this article] (2019). 5-hydroxymethylcytosine marks mammalian origins acting as a barrier to replication. Scientific Reports. 9. doi: 10.1038/s41598-019-47528-3. Full text in Research Archive Show summary

  In most mammalian cells, DNA replication occurs once, and only once between cell divisions. Replication initiation is a highly regulated process with redundant mechanisms that prevent errant initiation events. In lower eukaryotes, replication is initiated from a defined consensus sequence, whereas a consensus sequence delineating mammalian origin of replication has not been identified. Here we show that 5-hydroxymethylcytosine (5hmC) is present at mammalian replication origins. Our data support the hypothesis that 5hmC has a role in cell cycle regulation. We show that 5hmC level is inversely proportional to proliferation; indeed, 5hmC negatively influences cell division by increasing the time a cell resides in G1. Our data suggest that 5hmC recruits replication-licensing factors, then is removed prior to or during origin firing. Later we propose that TET2, the enzyme catalyzing 5mC to 5hmC conversion, acts as barrier to rereplication. In a broader context, our results significantly advance the understating of 5hmC involvement in cell proliferation and disease states.

• Chymkowitch, Pierre & Enserink, Jorrit (2018). Regulation of tRNA synthesis by posttranslational modifications of RNA polymerase III subunits. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms. ISSN 1874-9399. 1861(4), p. 310–319. doi: 10.1016/j.bbagrm.2017.11.001. Full text in Research Archive Show summary

  RNA polymerase III (RNAPIII) transcribes tRNA genes, 5S RNA as well as a number of other non-coding RNAs. Because transcription by RNAPIII is an energy-demanding process, its activity is tightly linked to the stress levels and nutrient status of the cell. Multiple signaling pathways control RNAPIII activity in response to environmental cues, but exactly how these pathways regulate RNAPIII is still poorly understood. One major target of these pathways is the transcriptional repressor Maf1, which inhibits RNAPIII activity under conditions that are detrimental to cell growth. However, recent studies have found that the cell can also directly regulate the RNAPIII machinery through phosphorylation and sumoylation of RNAPIII subunits. In this review we summarize post-translational modifications of RNAPIII subunits that mainly have been identified in large-scale proteomics studies, and we highlight several examples to discuss their relevance for regulation of RNAPIII.

• Kruitwagen, Tom; Chymkowitch, Pierre; Denoth-Lippuner, Annina; Enserink, Jorrit & Barral, Yves (2018). Centromeres License the Mitotic Condensation of Yeast Chromosome Arms. Cell. ISSN 0092-8674. 175(3), p. 780–795.e15. doi: 10.1016/j.cell.2018.09.012. Full text in Research Archive Show summary

  During mitosis, chromatin condensation shapes chromosomes as separate, rigid, and compact sister chromatids to facilitate their segregation. Here, we show that, unlike wild-type yeast chromosomes, non-chromosomal DNA circles and chromosomes lacking a centromere fail to condense during mitosis. The centromere promotes chromosome condensation strictly in cis through recruiting the kinases Aurora B and Bub1, which trigger the autonomous condensation of the entire chromosome. Shugoshin and the deacetylase Hst2 facilitated spreading the condensation signal to the chromosome arms. Targeting Aurora B to DNA circles or centromere-ablated chromosomes or releasing Shugoshin from PP2A-dependent inhibition bypassed the centromere requirement for condensation and enhanced the mitotic stability of DNA circles. Our data indicate that yeast cells license the chromosome-autonomous condensation of their chromatin in a centromere-dependent manner, excluding from this process non-centromeric DNA and thereby inhibiting their propagation.

• Herrera, Maria Carmen; Chymkowitch, Pierre; Robertson, Joseph; Eriksson, Jens; Bøe, Stig Ove & Alseth, Ingrun [Show all 7 contributors for this article] (2018). Cdk1 gates cell cycle-dependent tRNA synthesis by regulating RNA polymerase III activity. Nucleic Acids Research (NAR). ISSN 0305-1048. 46(22), p. 11698–11711. doi: 10.1093/nar/gky846. Full text in Research Archive Show summary

  tRNA genes are transcribed by RNA polymerase III (RNAPIII). During recent years it has become clear that RNAPIII activity is strictly regulated by the cell in response to environmental cues and the homeostatic status of the cell. However, the molecular mechanisms that control RNAPIII activity to regulate the amplitude of tDNA transcription in normally cycling cells are not well understood. Here, we show that tRNA levels fluctuate during the cell cycle and reveal an underlying molecular mechanism. The cyclin Clb5 recruits the cyclin dependent kinase Cdk1 to tRNA genes to boost tDNA transcription during late S phase. At tDNA genes, Cdk1 promotes the recruitment of TFIIIC, stimulates the interaction between TFIIIB and TFIIIC, and increases the dynamics of RNA polymerase III in vivo. Furthermore, we identified Bdp1 as a putative Cdk1 substrate in this process. Preventing Bdp1 phosphorylation prevented cell cycle-dependent recruitment of TFIIIC and abolished the cell cycle-dependent increase in tDNA transcription. Our findings demonstrate that under optimal growth conditions Cdk1 gates tRNA synthesis in S phase by regulating the RNAPIII machinery, revealing a direct link between the cell cycle and RNAPIII activity.

• Zimmermann, Christine; Llorente, Ignacio Garcia; Omerzu, Manja; Chymkowitch, Pierre; Zhang, Beibei & Enserink, Jorrit (2017). Mapping the synthetic dosage lethality network of CDK1/CDC28. G3: Genes, Genomes, Genetics. 7(6), p. 1753–1766. doi: 10.1534/g3.117.042317. Full text in Research Archive Show summary

  Cdk1 (Cdc28 in yeast) is a cyclin-dependent kinase (CDK) essential for cell cycle progression and cell division in normal cells. However, CDK activity also underpins proliferation of tumor cells, making it a relevant study subject. While numerous targets and processes regulated by Cdc28 have been identified, the exact functions of Cdc28 are only partially understood. To further explore the functions of Cdc28, we systematically overexpressed ∼4800 genes in wild-type (WT) cells and in cells with artificially reduced Cdc28 activity. This screen identified 366 genes that, when overexpressed, specifically compromised cell viability under conditions of reduced Cdc28 activity. Consistent with the crucial functions of Cdc28 in cell cycle regulation and chromosome metabolism, most of these genes have functions in the cell cycle, DNA replication, and transcription. However, a substantial number of genes control processes not directly associated with the cell cycle, indicating that Cdc28 may also regulate these processes. Finally, because the dataset was enriched for direct Cdc28 targets, the results from this screen will aid in identifying novel targets and process regulated by Cdc28.

• Enserink, Jorrit (2017). Regulation of cellular processes by SUMO: Understudied topics. Advances in Experimental Medicine and Biology. ISSN 0065-2598. 963, p. 89–97. doi: 10.1007/978-3-319-50044-7_5. Full text in Research Archive
• Pietarinen, Paavo O; Eide, Christopher A; Ayuda-Duran, Maria del Pilar; Potdar, Swapnil; Kuusanmäki, Heikki & Andersson, Emma I [Show all 18 contributors for this article] (2017). Differentiation status of primary chronic myeloid leukemia cells affects sensitivity to BCR-ABL1 inhibitors. OncoTarget. 8(14), p. 22606–22615. doi: 10.18632/oncotarget.15146. Full text in Research Archive Show summary

  Tyrosine kinase inhibitors (TKI) are the mainstay treatment of BCR-ABL1-positive leukemia and virtually all patients with chronic myeloid leukemia in chronic phase (CP CML) respond to TKI therapy. However, there is limited information on the cellular mechanisms of response and particularly on the effect of cell differentiation state to TKI sensitivity in vivo and ex vivo/in vitro. We used multiple, independent high-throughput drug sensitivity and resistance testing platforms that collectively evaluated 295 oncology compounds to characterize ex vivo drug response profiles of primary cells freshly collected from newly-diagnosed patients with BCR-ABL1-positive leukemia (n = 40) and healthy controls (n = 12). In contrast to the highly TKI-sensitive cells from blast phase CML and Philadelphia chromosome-positive acute lymphoblastic leukemia, primary CP CML cells were insensitive to TKI therapy ex vivo. Despite maintaining potent BCR-ABL1 inhibitory activity, ex vivo viability of cells was unaffected by TKIs. These findings were validated in two independent patient cohorts and analysis platforms. All CP CML patients under study responded to TKI therapy in vivo. When CP CML cells were sorted based on CD34 expression, the CD34-positive progenitor cells showed good sensitivity to TKIs, whereas the more mature CD34-negative cells were markedly less sensitive. Thus in CP CML, TKIs predominantly target the progenitor cell population while the differentiated leukemic cells (mostly cells from granulocytic series) are insensitive to BCR-ABL1 inhibition. These findings have implications for drug discovery in CP CML and indicate a fundamental biological difference between CP CML and advanced forms of BCR-ABL1-positive leukemia.

• Chymkowitch, Pierre; P, Aurélie Nguéa; Aanes, Håvard; Robertson, Joseph; Klungland, Arne & Enserink, Jorrit (2017). TORC1-dependent sumoylation of Rpc82 promotes RNA polymerase III assembly and activity. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 114(5), p. 1039–1044. doi: 10.1073/pnas.1615093114. Full text in Research Archive
• Enserink, Jorrit (2015). Sumo and the cellular stress response. Cell Division. 10. doi: 10.1186/s13008-015-0010-1. Full text in Research Archive
• Chymkowitch, Pierre; P, Aurélie Nguéa & Enserink, Jorrit (2015). SUMO-regulated transcription: Challenging the dogma. Bioessays. ISSN 0265-9247. 37(10), p. 1095–1105. doi: 10.1002/bies.201500065. Full text in Research Archive
• Chymkowitch, Pierre; P, Aurélie Nguéa; Aanes, Håvard; Koehler, Christian; Thiede, Bernd & Lorenz, Susanne [Show all 9 contributors for this article] (2015). Sumoylation of Rap1 mediates the recruitment of TFIID to promote transcription of ribosomal protein genes. Genome Research. ISSN 1088-9051. 25(6), p. 897–906. doi: 10.1101/gr.185793.114. Full text in Research Archive
• Enserink, Jorrit (2014). Metabolic pathways further increase the complexity of cell size control in budding yeast. Microbial Cell (MIC). 1(9), p. 276–278. doi: 10.15698/mic2014.09.167. Full text in Research Archive
• Davydova, Erna; Ho, Angela Yeuan Yen; Malecki, Jedrzej Mieczyslaw; Moen, Anders; Enserink, Jorrit & Jakobsson, Magnus [Show all 8 contributors for this article] (2014). Identification and characterization of a novel evolutionarily conserved lysine-specific methyltransferase targeting eukaryotic translation elongation factor 2 (eEF2). Journal of Biological Chemistry. ISSN 0021-9258. 289(44), p. 30499–30510. doi: 10.1074/jbc.M114.601658. Full text in Research Archive
• Zimmermann, Christine; Santos, Aline; Gable, Kenneth; Epstein, Sharon; Gururaj, Charulatha & Chymkowitch, Pierre [Show all 16 contributors for this article] (2013). TORC1 Inhibits GSK3-Mediated Elo2 Phosphorylation to Regulate Very Long Chain Fatty Acid Synthesis and Autophagy. Cell reports. 5(4), p. 1036–1046. doi: 10.1016/j.celrep.2013.10.024. Full text in Research Archive
• Chymkowitch, Pierre & Enserink, Jorrit (2013). The cell cycle rallies the transcription cycle: Cdc28/Cdk1 is a cell cycle-regulated transcriptional CDK. Transcription. ISSN 2154-1264. 4(1), p. 3–6. doi: 10.4161/trns.22456. Full text in Research Archive
• Enserink, Jorrit & Kolodner, Richard D. (2012). What makes the engine hum: Rad6, a cell cycle supercharger. Cell Cycle. ISSN 1538-4101. 11(2), p. 249–252. doi: 10.4161/cc.11.2.19023. Full text in Research Archive
• Enserink, Jorrit (2012). Chemical genetics: budding yeast as a platform for drug discovery and mapping of genetic pathways. Molecules. ISSN 1431-5157. 17(8), p. 9258–9273. doi: 10.3390/molecules17089258. Full text in Research Archive
• Pultz, Dennis; Bennetzen, Martin V.; Rodkær, Steven Vestergaard; Zimmermann, Christine; Enserink, Jorrit & Andersen, Jens S. [Show all 7 contributors for this article] (2012). Global mapping of protein phosphorylation events identifies Ste20, Sch9 and the cell-cycle regulatory kinases Cdc28/Pho85 as mediators of fatty acid starvation responses in Saccharomyces cerevisiae. Molecular Biosystems. ISSN 1742-206X. 8(3), p. 796–803. doi: 10.1039/c2mb05356j. Full text in Research Archive
• Chymkowitch, Pierre; Eldholm, Vegard; Lorenz, Susanne; Zimmermann, Christine; Lindvall, Jessica M. & Bjørås, Magnar [Show all 8 contributors for this article] (2012). Cdc28 kinase activity regulates the basal transcription machinery at a subset of genes. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 109(26), p. 10450–10455. doi: 10.1073/pnas.1200067109. Full text in Research Archive
• Zimmermann, Christine; Chymkowitch, Pierre; Eldholm, Vegard; Putnam, Christopher D.; Lindvall, Jessica Margareta & Omerzu, Manja [Show all 9 contributors for this article] (2011). A chemical-genetic screen to unravel the genetic network of CDC28/CDK1 links ubiquitin and Rad6-Bre1 to cell cycle progression. Proceedings of the National Academy of Sciences of the United States of America (PNAS). ISSN 0027-8424. 108(46), p. 18748–18753. doi: 10.1073/pnas.1115885108. Full text in Research Archive
• Enserink, Jorrit & Kolodner, Richard D. (2010). An overview of Cdk1-controlled targets and processes. Cell Division. 5. doi: 10.1186/1747-1028-5-11. Full text in Research Archive
• Kats, Ellen S; Enserink, Jorrit; Martinez, Sandra & Kolodner, RD (2009). The Saccharomyces cerevisiae Rad6 Postreplication Repair and Siz1/Srs2 Homologous Recombination-Inhibiting Pathways Process DNA Damage That Arises in asf1 Mutants. Molecular and Cellular Biology. ISSN 0270-7306. 29(19), p. 5226–5237. doi: 10.1128/MCB.00894-09. Full text in Research Archive
• Enserink, Jorrit; Hombauer, Hans; Huang, Meng-Er & Kolonder, Richard D. (2009). Cdc28/Cdk1 positively and negatively affects genome stability in S. cerevisiae. Journal of Cell Biology. ISSN 0021-9525. 185(3), p. 423–437. doi: 10.1083/jcb.200811083. Full text in Research Archive
• Enserink, Jorrit; Smolka, Marcus B.; Zhou, Huilin & Kolodner, Richard D. (2006). Checkpoint proteins control morphogenetic events during DNA replication stress in Saccharomyces cerevisiae. Journal of Cell Biology. ISSN 0021-9525. 175(5), p. 729–741. doi: 10.1083/jcb.200605080. Full text in Research Archive
• Enserink, Jorrit; Smolka, Marcus B.; Chen, Sheng-hong; Maddox, Paul S.; Albuquerque, Claudio P. & Wei, Xiao X. [Show all 9 contributors for this article] (2006). An FHA domain–mediated protein interaction network of Rad53 reveals its role in polarized cell growth. Journal of Cell Biology. ISSN 0021-9525. 175(5), p. 743–753. doi: 10.1083/jcb.200605081. Full text in Research Archive
• Bryn, Tone; Mahic, Milada; Enserink, Jorrit; Schwede, Frank; Aandahl, Einar Martin & Tasken, Kjetil (2006). The cyclic AMP-Epac1-Rap1 pathway is dissociated from regulation of effector functions in monocytes but acquires immunoregulatory function in mature macrophages. Journal of Immunology. ISSN 0022-1767. 176. Full text in Research Archive
• Enserink, Jorrit; Price, L.; Methi, Trond; Mahic, Milada; Sonnenberg, A. & Bos, Johannes L. [Show all 7 contributors for this article] (2004). cAMP, Epac and Rap1 regulate adhesion to laminin-5 through the alfa3beta1 integrin but not the alfa6beta4 integrin. Journal of Biological Chemistry. ISSN 0021-9258. 279, p. 44889–44896. Full text in Research Archive
• Vang, Torkel; Abrahamsen, Hilde; Myklebust, Sondre; Enserink, Jorrit; Prydz, Hans Peter B & Mustelin, Tomas [Show all 8 contributors for this article] (2004). Csk knockdown by RNA interference augments T cell receptor-mediated signaling in normal, peripheral T cells. European Journal of Immunology. ISSN 0014-2980. p. 2191–2199. Full text in Research Archive
• Enserink, Jorrit; Rangarajan, Savithri; Kuiperij, Bea; Rooij, Johan de; Price, Leo S. & Schwede, Frank [Show all 7 contributors for this article] (2003). Cyclic AMP induces integrin-mediated cell adhesion through Epac and Rap1 upon stimulation of the β2-adrenergic receptor. Journal of Cell Biology. ISSN 0021-9525. 160(4), p. 487–493. doi: 10.1083/jcb.200209105. Full text in Research Archive
• Enserink, Jorrit; Bos, Johanes L.; Bruyn, K. de; Kuiperij, Bea; Rangarajan, Savithri & Riedl, John [Show all 9 contributors for this article] (2003). The role of Rap1 in integrin-mediated cell adhesion. Biochemical Society Transactions. ISSN 0300-5127. p. 83–86. Full text in Research Archive
• Enserink, Jorrit; Christensen, Anne Elisabeth; Rooij, Johan de; Triest, Miranda van; Schwede, Frank & Genieser, Hans-Gottfried [Show all 9 contributors for this article] (2002). A novel Epac-specific cAMP analogue demonstrates independent regulation of Rap1 and ERK. Nature Cell Biology. ISSN 1465-7392. 4(11), p. 901–906. Full text in Research Archive
• Enserink, Jorrit; Verschure, Pernette J.; Kraan, Ineke van der; Moné, Martijn J.; Manders, Erik M.M. & Driel, Roel van (2002). Large-scale Chromatin Organization and the Localization of Proteins Involved in Gene Expression in Human Cells. Journal of Histochemistry and Cytochemistry. ISSN 0022-1554. 50(10), p. 1303–1312. doi: 10.1177/002215540205001003. Full text in Research Archive
• Enserink, Jorrit; Staal, Ada; Stein, Janet L.; Stein, Gary S. & Wijnen, Andre J. van (2000). Molecular characterization of Celtix-1, a bromodomain protein interacting with the transcription factor interferon regulatory factor 2. Journal of Cellular Physiology. ISSN 0021-9541. 185(2), p. 269–279. doi: 10.1002/1097-4652(200011. Full text in Research Archive

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• Tislevoll, Benedicte Sjo; Hellesøy, Monica; Fagerholt, Oda Helen Eck; Gullaksen, Stein-Erik; Srivastava, Aashish & Birkeland, Even [Show all 24 contributors for this article] (2023). Author Correction: Early response evaluation by single cell signaling profiling in acute myeloid leukemia (Nature Communications, (2023), 14, 1, (115), 10.1038/s41467-022-35624-4). Nature Communications. 14(1). doi: 10.1038/s41467-023-37488-8. Full text in Research Archive
• Enserink, Jorrit (2022). Brukermedvirkning i Kreftforskning. Full text in Research Archive
• Enserink, Jorrit (2022). Brukermedvirkning - Forskernes perspektiv. Full text in Research Archive
• Enserink, Jorrit (2022). Novel Methods for Stratification of Acute Myeloid Leukemia. Full text in Research Archive
• Zhang, Beibei; Ayuda-Duran, Maria del Pilar; Piechaczyk, Laure Isabelle; Fløisand, Yngvar; Safont, Mireia Mayoral & Karlsen, Ida Tveit [Show all 14 contributors for this article] (2019). GRP94 rewires and buffers the FLT3-ITD signaling network and promotes survival of acute myeloid leukemic stem cells. Haematologica. ISSN 0390-6078. 104(5). doi: 10.3324/haematol.2019.220533. Full text in Research Archive
• Ayuda-Duran, Maria del Pilar; Zhang, B; Piechaczyck, L.; Popa, Mihaela Lucia; Tadele, Dagim Shiferaw & Rowe, Alexander D. [Show all 12 contributors for this article] (2017). a precision medicin platform for acute myeloid leukemia to help unraveling the molecular addictions of FLT3-ITD-driven AML. Full text in Research Archive Show summary

  Acute myeloid leukemia (AML) is an aggressive disease with poor prognosis (Tzelepis et al. 2016). No single driver mutation is present in all cases of AML, making its treatment a challenge (The Cancer Genome Atlas Research 2013). Current standard of care for AML is an aggressive cytostatics-based treatment that has remained unchanged for the past 30 years (Longo et al. 2015). Weak or elderly patients might not be eligible for intensive treatment, leading to poor survival rates. Many such patients are labeled as “untreatable”, although a portion of them could benefit from specific, individualized treatment. A precision medicine strategy can help to find the specific treatment for these ‘untreatable’ AML patients. Aims Drug-driven personalized medicine aims to directly test the sensitivity of primary cancer cells taken from individual AML patients to a selection of targeted cancer drugs, compare these results with drug sensitivities of healthy donor samples and select the most effective drug for each patient. This approach considers any combination of mutations or epigenetic changes that might not be found in the standard sequencing panels, an advantage when dealing with such a heterogeneous disease. Proof of principle of this strategy was recently demonstrated by FIMM (Helsinki, Finland) (Pemovska et al. 2013), not only providing immediate clinical benefit to leukemia patients, but also identifying drugs that can potentially be repurposed for future treatment of patients. Methods We have established a drug-driven personalized medicine platform for AML where we check the ex-vivo drug sensitivity and resistance of bone marrow primary cells to a panel of around 400 drugs and drug combinations covering the standard of care treatments, cancer chemotherapeutics as well as many clinically available and emerging molecularly targeted compounds. We calculate the IC50 values for all the drugs for each individual donor or patient, and then the differential drug sensitivity scores, selecting the drugs that affect preferentially the cancer cells when compared with healthy cells. To date we have successfully processed 6 healthy donors and 66 AML samples identifying subgroups of patients who respond with a similar dynamic to certain classes of drugs, as the subgroup of cells carrying internal tandem duplications in the receptor tyrosine kinase FLT3 (FLT3-ITD). Results FLT3 activating mutations, particularly FLT3-ITD, have been observed in approximately 30% of AMLs (The Cancer Genome Atlas Research 2013), and are associated with increased risk of relapse and poor clinical outcome (Abu-Duhier et al. 2008). The cellular pathways that support FLT3-ITD-driven cell proliferation and survival remain poorly understood. We discovered that FLT3-ITD-expressing AML blasts show an enhanced sensitivity to HSP90 inhibitors such as Ganetespib compared to healthy donors and any other subgroups of leukemia. In addition, HSP90 inhibitors specifically sensitize FLT3-ITD-expressing bone marrow-derived cells to TKIs, whereas cells derived from healthy donors are unaffected. HSP90 inhibitors also preferentially eradicate a population of patient-derived FLT3-ITD+ AML cells expressing leukemic stem cell markers. Conclusion In summary, our study reveals a molecular basis for HSP90 addiction of FLT3-ITD-driven AML and provides a rationale for treatment of this form of AML with HSP90 inhibitors. Session topic: 3. Acute myeloid leukemia - Biology Keyword(s): Flt3-ITD, AML

• Enserink, Jorrit (2013). Cdk1 is part of a network of priming kinases that directly regulate the basal transcription machinery. Yeast. ISSN 0749-503X. 30, p. 66–66. Full text in Research Archive
• Zimmermann, Christine; Chymkowitch, Pierre; Eldholm, Vegard; Putnam, Christopher D.; Lindvall, Jessica M. & Omerzu, Manja [Show all 9 contributors for this article] (2012). A chemical-genetic screen to unravel the genetic network of CDC28/CDK1 links ubiquitin and Rad6-Bre1 to cell cycle progression. The FASEB Journal. ISSN 0892-6638. 26. Full text in Research Archive

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